Functionalized compositions for improved immobilization

ABSTRACT

The present invention relates to improved covalent coupling of two or more entities such as biomolecules, polymer compositions, organic/inorganic molecules/materials, and the like, including their combinations, through one or more novel reactive groups attached to linker groups of 2-1000 atoms length. The present invention also contemplates the use of bifunctional bridge molecules to link two or more entities, wherein the functional groups of the bridge molecules are the novel reactive groups of the present invention.

1. CROSS REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. provisional Application No.60/331,312, filed Nov. 14, 2001, the disclosure of which is herebyincorporated herein by reference in its entirety.

2. FIELD OF THE INVENTION

The present invention relates to improved covalent coupling of two ormore entities such as biomolecules, polymer compositions,organic/inorganic molecules/materials, and the like, including theircombinations, through one or more novel reactive groups attached tolinker groups of 2-1000 atoms length.

3. BACKGROUND OF THE INVENTION

The immobilization of entities (such as enzymes, antibodies, proteins,DNA, nucleotides, PNA, carbohydrates, fatty acids, lectins, peptides,receptors, chromophores, fluorophores, chemiluminescent compounds,dendrimers, J or H aggregates, cells, bacteria, viruses, wholeprokaryotic or eukaryotic organisms, membranes (synthetic or natural),fullerenes, nanotubes and the like) can be achieved by simple covalentreaction with an activated solid surface. For example, particles (e.g.,micro- and nano-spheres; metal particles comprised of one or more metalswith any size, shape, or composition;—semiconductor particles,molecularly imprinted polymers (MIPS), magnetic particles; or dyedmaterials) or microtiter plates are a common solid matrix in manyimmobilization systems. Preparing and maintaining the active,functionalized surface is an important factor to assure immobilizationof sufficient biological material for development of a sensitive assay.Current immobilization procedures of biomolecules on solid surfacesgenerally involve reactions of an activated amino or carboxyl groupderivatized solid surface with amino- or thiol-modified biomolecules.After activation, or after introduction of a functionalized spacer,these groups offer direct attachment sites. Most of these functionalgroups (such as NHS esters, isothiocyanates, etc.) are prone tohydrolysis in an aqueous environment and become non-reactive (i.e.,chemically inactive) in a matter of less than an hour.

Reactive or functionalized microspheres are conventionally produced viacopolymerization of suitably functionalized monomers, or viapost-chemical modification of preformed microspheres.Post-functionalization is a popular method for preparing reactiveparticles as earlier described by Upson (J. Polym. Sci., Polym. Symp.1985, 72, 45).

In the last three decades the advancements in the field of affinitychromatography, solid-phase synthesis, and immobilization ofbio-macromolecules, such as proteins, oligonucleotides and the like,have led to microsphere-based biomedical applications. More recent workon the production and evaluation of a variety of tailor-made particleshas been reported by several groups including Margel et al., (J. Polym.Sci. 1991, A-29, 347-355; Anal. Biochem. 1981, 128, 342-350), Ugelstadet al., (Makromol. Chem. 1979, 180, 737-44; Adv. Colloid Interface Sci.1980, 13, 102-140), and Rembaum et al. (Br. Polym. J. 1978, 10, 275-280;J. Macromol. Sci. Chem. 1979, A-13, 603-632). A review by R. Arshady,(Biomaterials, 1993, 14, 5-15) describes the synthesis andphysico-chemical properties of reactive and labeled microspheres.

Assays based on fluorescent microspheres for multiplexed analysis havebeen reported by several groups (Fulton et al., Clin. Chem. 1997, 43,1749-56; Kettman et al., Cytometry, 1998, 33, 234-43; McDade et al.,Med. Dev. Diag. Indust. 1997, 19(4), 75-82; McHugh, Methods Cell Biol.1994, 42, 575-95; Nikiforov et al., Nucleic Acid Res. 11994, 22,4167-75; U.S. Pat. No. 6,449,562; U.S. Pat. No. 5,981,180; U.S. Pat. No.6,046,807; U.S. Pat. No. 6,057,107; U.S. Pat. No. 6,268,222; U.S. Pat.No. 6,366,354; U.S. Pat. No. 6,411,904; U.S. Pat. No. 5,736,330; U.S.Pat. No. 6,139,800).

Fray et al have reported a strategy in which particles are pre-activatedwith hydrolysis-resistant aldehyde functional groups but low reactionyields of <8% have been observed with these microspheres (BioconjugateChem. 1999, 10, 562-71). Milton of Beckman Coulter, Inc. has reported areaction between an acyl fluoride activated polymer-surface and an aminoderivatized biomolecule at room temperature (U.S. Pat. No. 6,146,833;Nov. 14, 2000). The use of fluorophenyl resins in the solid phasesynthesis of amides, peptides, hydroxamic acids, amines, urethanes,carbonates, sulfonamides and alpha-substituted carbonyl compounds hasbeen published (WO 99/67228).

Medvedkin et al. have used sulfo-tetrafluorophenyl activated esters inpeptide synthesis and demonstrated their reactivity combined with goodstability under aqueous storage conditions (Bioorg. Khim. 1995, 21(9),684-90). Apparently, the pre-activation of polystyrene surfaces withthis reagent has not yet been reported prior to the present application.

Hoechst claimed the use of reactive vinyl sulfone (VS)-modified dyes fordyeing of cellulose and wool fibers in 1950 (DBP 960,534). A review bySiegel gives a complete account of reactive dyes based on vinyl sulfones(VS) and its protected 2-sulfatoethyl and 2-thiosulfatoethyl sulfones (ESiegel in The Chemistry of Synthetic Dyes Vol. VI, (Ed K Venkataraman);2-108, Academic Press, 1972). Sterling Winthrop Inc, has demonstratedmodification of proteins with PEG-supported vinyl sulfone (U.S. Pat. No.5,414,135).

The most frequently used method to immobilize biomolecules (such asoligonucleotides, proteins, or carbohydrates) onto fluorescentmicrospheres is by activating surface carboxy groups. The activationrequires excess EDC and a coupling pH of 4 to 6. The reaction involvesthe intermediate formation of an activated O-acylurea derivative betweenthe carbodiimide and carboxyl functions. A subsequent nucleophilicattack by the primary nitrogen of the amino-groups of the biomoleculebrings about the formation of the amide linkage with the release of thesubstituted urea. The optimum pH for the formation of O-acylurea isabout pH 4-5. The intermediate has an extremely short half-life andrapidly undergoes hydrolysis or rearranges to give the N-acylurea adductThe primary amino group of the nucleophile is predominantly protonatedat about pH 4-5 and is thus mostly unreactive. These limitations canseverely restrict coupling yields. At low pH, the nucleic acid basesundergo intensive protonation. Such type of protonation induces a DNAmelting that exposes the hydrophobic core of the helix, enhancingnonspecific hydrophobic interactions with the solid matrix. Despitethese drawbacks, EDC-mediated coupling currently is the major mode ofcovalent immobilization of biomolecules to solid surfaces. (Hermanson,G. T. in Bioconjugate Techniques, Academic Press; N.Y. 1996; AndreasFrey et. al., Bioconjugate Chem. 1999, 10, 562-71; Maxime A. Gilles et.al., Anal. Biochem., 1990, 184, 244-48; Vivien W. F. Chan et. al.,Biochem. Biophys. Res. Communications, 1988, 151(2), 709-16; Ivan L.Valuev et al., Biomaterials, 1998, 19, 41-43.)

The citations of the various references described above and throughoutthis application are not to be taken as admissions that these referencesconstitute prior art for the present invention. However, each of thecited references is incorporated in its entirety by reference in thepresent application.

4. SUMMARY OF THE INVENTION

The present invention is based, at least in part, upon improved methodsand compositions for covalent coupling of two or more entities (B, B′,etc.) such as biomolecules, polymer compositions, organic and/orinorganic molecules and/or materials, etc., through one or more “novelreactive groups” (Structures 1-6). The illustrations and examplesprovided herein are not intended to limit the scope of the invention inany way.

Entities B, B′, etc., under the present invention comprise, but are notlimited to, glass, quartz, monomer, polymer, dendrimer, MIPS, membranes,metal, clay, diatomaceous earth, particle (dyed or undyed), particle(magnetic or non-magnetic), particle (micro- or nanospheres),fullerenes, nanotubes, biomolecule, chromophore, fluorophore,chemiluminescent compound, semiconductor particles, semiconductornanocrystals (quantum dots), J- or H-aggregates, cells, organisms,bacteria, viruses, or any combination thereof. Entities B, B′, etc., canbe the same or different, and can be functionalized ornon-functionalized.

The novel reactive groups of the present invention are conjugated toentities B, B′, etc., by way of a linker, (L)_(n), where L is ahydrocarbon linker with n number of atoms (e.g., 2 to 1000) of H, C, O,N, Si, P and S in straight or branched chains, rings, or combinationsthereof.

In some embodiments, one or more entities B, B′, etc., arenucleophile-containing entities, i.e., they contain hydroxyl, amine,thiol . . . etc., groups, or the entities are conjugated to such groups.In such cases, attachment of the novel reactive groups may beaccomplished by the chemical reaction of the electrophilic reactivegroup of one or more of Structures 1-6 with the nucleophilic groupcontained on or within the entity. Such chemical reactions include, butare not limited to, nucleophilic addition or nucleophilic-based reactionknown to a person of ordinary skill in the art, substitution and/ordisplacement.

By way of a non-limiting example, a reaction of the present inventionwhereby two entities, B and B′, are cross-linked via one or more ofStructures 1-6. Any nucleophile- or electrophile-containing groups aretermed A, A′, etc., where A and/or A′ are a novel reactive group, orcombination thereof, discussed in the present invention and/or anucleophile (e.g., alcohol, amine, thiol . . . etc.), respectively. Aand A′ can be the same or different novel reactive group and/or the sameor different nucleophile. B and B′ can either be the same and/ordifferent entities. Several possible combinations of such elements arediscussed, below.

In one embodiment, one entity B, a polymeric microsphere, is conjugatedwith an electrophile-containing group of one of Structures 1-6 throughthe group's respective linker R₁-R₆. A second entity, B′, asemiconductor nanoparticle, is conjugated with a nucleophilic group atits surface. A straightforward nucleophilic substitution reactionresults in the linking of B with B′ by way of the linker.

In yet another embodiment of a reaction linking B and B′, where A and A′are both novel reactive groups of Structures 1-6, or a combinationthereof, a bifunctional linker or bridge molecule is used to covalentlycouple the two or more entities. In one such embodiment, thebifunctionality of the linker is nucleophilic (e.g., amine, thiol,etc.). In other words, the bridge molecule contains two or morenucleophilic groups, one of which reacts with each of A and A′ such thatB and B′ are linked through the combined length of the linker arms of Aand A′ and the length of the bridge molecule.

In yet another embodiment, B and B′ contain A and A′, respectively,which are both nucleophiles. In this embodiment, a bifunctional linkeror bridge molecule is used to couple the two or more entities wherebythe bifunctionality of the linker or bridge molecule are one or morenovel electrophilic reactive groups of Structures 1-6, where thosegroups can be the same or different novel reactive groups. The bridgemolecule may or may not be constructed by joining the free ends of thelinkers R₁-R₆ of the respective electrophilic reactive groups ofStructures 1-6. Following the reaction of these elements, B and B′ arelinked via the bifunctional bridge molecule binding covalently to theirrespective nucleophilic groups. In another version of this embodiment,if A and A′ are both nucleophiles, then a bifunctional linker or bridgemolecule is used to couple the two or more entities wherein C and/or C′are a functional group or groups (e.g., NHS ester, isothiocyanate,sulfonyl chloride, etc.) known to react with nucleophiles A and A′. Cand C′ can be the same or different functional groups which are attachedto the linker or bridge molecule by way of one or more (n) novelelectrophilic reactive groups of Structures 1-6 where n is the number ofnovel electrophilic reactive groups.

In particular, the present invention is directed toward novel conjugatedcompositions comprising one or more, in any combination, of Structures1-6:

wherein:

-   -   n is 0, 1, 2, or 3;    -   X and Y are oxygen and/or sulfur in any combination;    -   X₂ and X₃ are one or more halogens, preferably chlorine or        fluorine;    -   Y₂ is nitrogen or carbon;    -   arom is a substituted or unsubstituted phenyl, naphthyl or other        polycyclic aromatic ring structure;    -   Z is a halide, preferably chloride or fluoride,        2,3,5,6-tetrafluoro-4-sulfo-phenoxide, N-hydroxysuccinimide or        other electrophilic (nucleofugal) group; and    -   R₁-R₆ are hydrocarbon linker groups containing from 2-1000        atoms, optionally containing one or more halogen or heteroatoms        selected from the group consisting of O, N, Si, P and S; in        straight or branched chains, rings, or combinations thereof; and        wherein the one or more, in any combination, of Structures 1-6        are connected through their respective linker groups, R₁-R₆, to        at least one entity B, wherein B is:    -   a 2-D film or substrate;    -   a micro- or nano- particle of any size or shape composed of        organic polymer, MIPS, glass, metal, clay, resin, diatomaceous        earth, zeolite, inorganic crystal, semiconductor particle,        semiconductor nanocrystal, magnetic particle, fullerene,        nanotube, or any combination thereof;    -   an enzyme, antibody, protein, DNA, RNA, nucleotide, PNA,        carbohydrate, fatty acid, lectin, peptide, receptor, dendrimer,        cell, bacteria, virus, whole prokaryotic or eukaryotic organism,        synthetic or natural membrane, biotin, hapten, organic monomer        or polymer, or any combination thereof;    -   a chromophore, fluorophore, bio- or chemi-luminescent compound,        J or H aggregate;    -   one or more of Structures 1-6 connected through their respective        linker groups R₁-R₆; or any combination thereof.

In yet another further embodiment, the present invention is directed tonovel compositions as described above wherein R₁-R₆ contain 2-100 atoms,or more preferably wherein R₁-R₆ contain 2-10 atoms.

The present invention also encompasses compositions comprising theStructures 1-6 noted above, wherein R₁-R₆ comprise hydrocarbon linkergroups containing, optionally, one or more halogen or heteroatomsselected from the group consisting of O, N, Si, P and S; in straight orbranched chains, rings, or combinations thereof containing from 2-1000atoms, preferably 2-100 atoms, or more preferably wherein R₁-R₆ contain2-10 atoms.

The present invention also is directed toward compositions as describedabove wherein B is a polymeric microsphere or nanosphere. Even morepreferred is an embodiment wherein the polymeric microsphere furthercomprises polystyrene/divinyl benzene and/or carboxyl functional groupsat least on its surface, and even more preferred is an embodimentwherein the microsphere further comprises one or more fluorescent dyesin distinguishable ratios.

As noted above, the present invention relates, in a preferredembodiment, to functionalized microspheres. A series of reactivefunctional groups has been evaluated on polystyrene-based microspheresfor their ability to immobilize biomolecules, which biomoleculescomprise prokaryotic or eukaryotic cells, transgenic cells, organisms,bacteria, viruses, plasmids, expression vectors, enzymes, proteins,fusion proteins, antibodies, chimeric antibodies, DNA, RNA, PNA, fattyacids, lectins, peptides, and receptors, or any combination thereof.Activated oxocarbon acids (erg., mono-fluoro squaric acid (MFS)),tetra-fluoro-sulfophenyl ester (TFS), vinyl sulfone (VS),dihaloquinoxaline, sulfonyl fluoride, cyanuric acid halide andhalopyrimidine show improved performance for immobilizing biomoleculesas they (a) spontaneously react with nucleophilic groups ofbiomolecules, (b) show substantially improved stability in aqueousmedia, (c) form stable conjugates with biomolecules, (d) require noadditional activating reagents and (e) may provide more specificconjugation (i.e., reduced non-specific interaction/binding with solidsubstrates) thus protecting the integrity of the biomolecule.

In yet another embodiment, a novel reactive group can be attached firstto a biomolecule and then coupled to a solid support containingnucleophilic groups. Also disclosed are new linker systems aimed atimproving the coupling yields of biomolecules to solid surfaces.

In particular, the present invention is directed toward a method forcoupling two or more entities together by providing one or moreconjugate compositions as described above having one or more, in anycombination, of Structures 1-6 connected through their respective linkergroups, R₁-R₆, to at least one entity B; providing one or morenucleophile-containing entities comprised of:

-   -   a 2-D film or substrate;    -   a micro- or nano-particle of any size or shape, composed of        organic polymer, MIPS, glass, metal, clay, resin, diatomaceous        earth, zeolite, inorganic crystal (including semiconductors,        semiconductor nanocrystals, and magnetic particles), fullerene,        nanotube or any combination thereof;    -   an enzyme, antibody, protein, DNA, RNA, nucleotide, PNA,        carbohydrate, fatty acid, lectin, peptide, receptor,        chromophore, fluorophore, bio- or chemi-luminescent compound, J        or H aggregate, cell, bacteria, virus, whole prokaryotic or        eukaryotic organism, synthetic or natural membrane, biotin,        hapten, organic monomer or polymer, or dendrimer, or any        combination thereof; and        reacting the one or more conjugate compositions with the one or        more nucleophile-containing entities to produce at least one        entity B linked through one or more linker arms of Structures        1-6 to said one or more nucleophile-containing entities.

In another embodiment, the present invention encompasses a method forthe synthesis of compositions of noted above wherein the one or more, inany combination, of Structures 1-6 are conjugated to the entity B beforethe fabrication of the entity B; during the fabrication of the entity B;are conjugated to the entity B after the fabrication of entity B.

Another preferred embodiment of the present invention is directed towarda method of crosslinking one or more nucleophile-containing entitiescomprising reacting a composition of Structure 1, as described above,wherein:

-   -   (a) n is 0, 1, 2, or 3    -   (b) X and Y are oxygen and/or sulfur in any combination;    -   (c) Z and R₁ are halogen (including chloride and fluoride);        2,3,5,6-tetrafluoro-4-sulfo-phenoxide; N-hydroxysuccinimide; and        similar nucleofugal groups or any combination thereof;    -   with one or more nucleophile-containing entities, comprised of:    -   a 2-D film or substrate;    -   a micro- or nano-particle of any size or shape, composed of        organic polymer, MIPS, glass, metal, clay, resin, diatomaceous        earth, zeolite, inorganic crystal (including semiconductors,        semiconductor nanocrystals, and magnetic particles), fullerene,        nanotube or any combination thereof;    -   an enzyme, antibody, protein, DNA, RNA, nucleotide, PNA,        carbohydrate, fatty acid, lectin, peptide, receptor,        chromophore, fluorophore, bio- or chemi-luminescent compound, J        or H aggregate, cell, bacteria, virus, whole prokaryotic or        eukaryotic organism, synthetic or natural membrane, biotin,        hapten, organic monomer or polymer, or dendrimer or any        combination thereof;        to provide one or more crosslinked nucleophile-containing        entities.

In yet an even further embodiment, the present invention is directedtoward the use of Structures 1-6 in the creation of bridge molecules forlinking two or more entities together, or compositions comprising one ormore of Structures 1-6 as bridge molecules. Various embodiments of thepresent invention include multifunctional bridge molecules of two ormore of Structures 1-6 joined through their respective linker groupsR₁-R₆, in an end-to-end fashion, in a branched chain, or in dendriticfashion. Such bridge molecules may be used to link together covalentlytwo or more entities having nucleophilic groups by straightforwardchemical reactions such as nucleophilic addition or substitution or anyother applicable chemical reaction known to a person of ordinary skillin the art.

In yet another variation of this invention, a multifunctional bridgemolecule is provided wherein the functional groups are one of more ofStructures 1-6 and one or more nucleophilic groups. Such bridgemolecules may be used to link together covalently one or more entitieshaving nucleophilic groups with one or more entities conjugated to oneor more of Structures 1-6 by straightforward chemical reactions such asnucleophilic addition or substitution, wherein the entity(ies) havingnucleophilic groups react with the bridge group functionality(ies) ofStructures 1-6, and the entity(ies) having reactive groups of Structures1-6 react with the nucleophilic bridge group functionality(ies) to yieldtwo or more entities linked together.

Compositions of such multifunctional bridge groups are also envisioned.A bridge group composition is envisioned wherein one or more ofStructures 1-6, in any combination, are conjugated by their respectivelinker groups R₁-R₆ to one or more nucleophilic groups, wherein if twoor more of Structure 1-6 are joined together, they are joined togetherthrough their respective linker groups R₁-R₆, wherein the joining is oneor more of end-to-end, branched, or dendritic, in any combination.

5. BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows a comparison of the COOH-functionalized microsphere, EDCcoupling method (A) to mono-fluoro squaric acid-functionalizedmicrospheres (MFS) (B) over time (accelerated at 25° C.). The novelpre-activated microspheres (B) provide more reproducible couplingday-to-day than the standard EDC-mediated reactions (A).

FIG. 2 shows a stability study of vinyl sulfone (VS)-functionalizedmicrospheres stored in buffer, pH 6 at 4° C.

FIG. 3 shows an accelerated stability study of mono-fluoro squaric acid(MFS)-functionalized microspheres stored dry.

FIG. 4 shows an accelerated stability study of mono-fluoro squaric acid(MFS)-functionalized microspheres stored dry over a longer time periodthan shown in FIG. 3.

FIG. 5 shows an accelerated stability study of tetra-fluoro-sulfophenylester (TFS)-functionalized microspheres stored dry.

FIG. 6 shows an accelerated stability study of vinyl sulfone(VS)-functionalized microspheres stored dry.

FIG. 7 shows a coupling titration of an amino-functionalized DNA probeon (A) COOH-functionalized microspheres (EDC-mediated reaction) vs. (B)mono-fluoro squaric acid (MFS)-functionalized microspheres (spontaneousreaction) methods. Both coupling titrations were performed at 25° C. TheDNA compliment target concentration for the assay was 20 fmoles at ahybridization temperature of 55° C. The COOH-EDC method (A) yields anon-linear response to the amount of probe coupled to the microspheres.The mono-fluoro squaric acid-functionalized microsphere's probetitration (B) is more linear. These results are reproducible and may bethe result of a more specific coupling. Note: 25° C. is not an optimalcoupling temperature for the mono-fluoro squaric acid-functionalizedmicrospheres. Signal is expected to improve with optimization of allparameters.

6. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS 6.1 FunctionalGroups

Because of the shortcomings of current coupling methods—lack ofstability or inability to spontaneously react with biomolecules inaqueous media or both—the inventors decided to introducehydrolysis-resistant, ready to use, pre-activated microspheres, for theimmobilization of biomolecules. Table 1 is a partial, non-limiting, listof such novel reactive microspheres.

Sulfonyl fluorides are known to be more stable in an aqueous environmentthan sulfonyl chlorides (Table 1, 1a-1d) and the aromatic versions aremore stable as compared to their aliphatic counter parts. Several routesstarting either from acids or acid chlorides were used to synthesizesulfonyl fluorides (Table 1, 2a-2e) on the surface of polystyrenemicrospheres.

The cyclic oxo-carbon acids (deltic, squaric, croconic and rhodizonic)have two acid equivalents and 1-4 carbonyl groups in a ring. Theinventors have used one of the acid equivalents to connect the ring toone of our linker molecules and activated the other to a reactivederivative. Several routes to synthesize squaric acid derivatizedmicrospheres are provided in Table 1 (-3a-3e). The resulting activatedbeads are very reactive with amine containing molecules and can bestored on a long term basis if kept dry. This class of reactive groupcan also be used as a replacement for NHS esters and the like toactivate dyes and biomolecules.

Cyanuric fluoride can react with up to three equivalents of amine,replacing the fluorine atoms with the nitrogen atoms of the amines. Theinventors have isolated microspheres in which cyanuric fluoride wasreacted with one equivalent of an amine linker, which was attached to amicrosphere (Table 1, 4). The second and third fluorine are stillavailable for reaction with bio-molecules. Related molecules such ascyanuric chloride, 2,4,6-trichloro pyrimidine or2,4,6-trifluoropyrimidine are used similarly.

Vinyl sulfone (VS) microspheres were generated by reacting divinylsulfone with microspheres containing hydroxy, amino or thiol groups(Table 1, 5a-5b). The remaining vinyl moiety is available for reactionwith both thiols and amines. This group is less susceptible tohydrolysis, but requires a basic pH for reaction with amines. The vinylsulfone (VS) group can be protected from oxidation during long termstorage by reacting it with sodium thiosulfate as in Table 1, 5c. Thevinyl moiety is regenerated at about pH 9-10.

Perfluorinated phenols have been developed as hydrolysis resistantreplacements for N-hydroxysuccinimide for conventional couplingchemistries. The inventors reacted tetrafluoro-phenolsulfonic acid withcarboxylic acid groups directly on the surface of microspheres (Table 1,6) or on the end of a linker molecule. Fluorine atoms provide the moietywith a good leaving group and the sulfonic acid maintains the charge onthe surface of the microsphere, which is needed to disperse it in water.

6.2. Linkers

The overall performance of a functionalized microsphere is controlled byseveral parameters—microsphere charge, density of cross-linking,location, accessibility and chemical stability of functional groups,length, charge and nature of the linker group.

Linkers play an important role in bioconjugations. They are selectedbased not only on their length, but their chemical nature. The overallnature of the linker is known to govern the overall hydrophilicity orhydrophobicity of the reagent environment. It is well understood thatextended linkers can reduce the steric interferences between the analyteand the solid matrix.

Several different classes of linkers could be used to connect the abovementioned functional groups to microspheres. Examples of these linkersare shown in Table 2.

Ethylene glycol based linkers (Table 2, 1-3) are surface modifiers whichare known for improving the stability of hydrophilic surfaces.Additional stability is ensured by replacing CH₂ with CF₂. Straightchain polymethylenes (Table 2, 4) are other linkers that may be used toconnect the above mentioned functional groups to microspheres.

Diamines and hydrazides are known to provide hydrophobic surfaces (Table2, 5-8). Polyethylenimines (Table 2, 9) exhibit a ‘proton sponge’effect, which can be used to control the surface charge of themicrosphere. Polyamides and polysulfonamides (Table 2, 10-13) containacidic protons with a pKa of about 1-2. These linkers, therefore,provide polyanions at physiological pH and hence provide long storagestability. Dendrimers or highly branched linkers (Table 2, 14) are knownto adopt to well defined morphologies and provide a kind ofencapsulation to the reactive groups and hence protect them fromhydrolysis. DTPA (diethylene triamine pentaacetic acid) linkers (Table2, 1S) provide multiple carboxylates. These type of linkers are known toform stable metal complexes. Polyacrylic acid and polylysine chains(Table 2, 16-17) can be introduced to improve the degree ofimmobilization.

6.3. Examples of Specific Application

The following are examples of specific applications of the presentinvention. These examples are not intended to limit the scope of theinvention in any way.

Example 6.3.1

This example relates to, but is not limited to, the use offunctionalized, or pre-activated, microspheres for covalentimmobilization of biomolecules.

-   -   (a) A solid support comprised of a polymeric microsphere,        preferably polystyrene/divinyl-benzene, containing carboxyl        functional groups at least on its surface.    -   (b) The solid support (a) where the solid support contains one        or more fluorescent dyes in distinguishable ratios.    -   (c) Solid support (b) where at least surface carboxyl groups        have been modified with a 4,7,10-trioxa-1,13-tridecanediamine        linker.    -   (d) Solid support (c) where the linker has been modified and/or        contains the novel reactive group mono-fluoro squaric acid        (MFS).    -   (e) A biomolecule, specifically an oligonucleotide probe,        containing a primary amine terminus.    -   (f) Spontaneous, covalent coupling of solid support (d) and        biomolecule (e) to form a stable, covalent bond.    -   (g) Use of the biomolecule-coupled solid support (f) in a single        or multiplexed DNA assay.

Example 6.3.2

This example relates to, but is not limited to, the use offunctionalized, or pre-activated, microspheres for covalentimmobilization of biomolecules.

-   -   (a) A solid support comprised of a polymeric microsphere,        preferably polystyrene/divinyl-benzene, containing carboxyl        functional groups at least on its surface.    -   (b) The solid support (a) where the solid support contains one        or more fluorescent dyes in distinguishable ratios.    -   (c) Solid support (b) where at least surface carboxyl groups        have been modified with a cystamine linker.    -   (d) Solid support (c) where the linker has been modified and/or        contains the novel vinyl sulfone (VS) reactive group.    -   (e) A biomolecule, specifically an antibody, containing a        primary amine or thiol.    -   (f) Spontaneous, covalent coupling of solid support (d) and        biomolecule (e) to form a stable, covalent bond.    -   (g) Use of the biomolecule-coupled solid support (f) in a single        or multiplexed immunoassay.

Example 6.3.3

This example relates to, but is not limited to, the use offunctionalized, or pre-activated, microspheres for covalentimmobilization of biomolecules.

-   -   a) A solid support comprised of a polymeric -microsphere,        preferably polystyrene/divinyl-benzene, containing carboxyl        functional groups at least on its surface.    -   b) The solid support (a) where the solid support contains one or        more fluorescent dyes in distinguishable ratios.    -   c) Solid support (b) where the carboxyl groups have been        modified to contain the novel tetra-fluoro-sulfophenyl ester        (TFS) reactive group.    -   d) A biomolecule, specifically an antigen, containing a primary        amine.    -   e) Spontaneous, covalent coupling of solid support (c) and        biomolecule (d) to form a stable, covalent bond.    -   f) Use of the biomolecule-coupled solid support (e) in a single        or multiplexed immunoassay.

Example 6.3.4

This example relates to, but is not limited to, the use of a solidsurface for covalent immobilization of functionalized, or pre-activatedbiomolecules.

-   -   a) A two-dimensional solid support comprised of quartz, and        containing hydroxyl functional groups at least on its surface.    -   b) Solid support (a) where at least surface hydroxyl groups have        been modified with aminopropyl-triethoxy silane, an        amino-terminated silane linker.    -   c) A biomolecule, specifically an oligonucleotide, where the        terminus has been modified to contain the novel reactive group        mono-fluoro squaric acid (MFS).    -   d) Spontaneous, covalent coupling of solid support (b) and        biomolecule (c) to form a stable, covalent bond.    -   e) Use of the biomolecule-coupled solid support (d) in a single        or multiplexed DNA assay.

Example 6.3.5

This example relates to, but is not limited to, the use offunctionalized, or pre-activated, microspheres for covalentimmobilization of semi-conductor nanoparticles.

-   -   a) A solid support comprised of a polymeric microsphere,        preferably polystyrene/divinyl-benzene, containing carboxyl        functional groups at least on its surface.    -   b) Solid support (a) where the carboxyl groups have been        modified to contain the novel vinyl sulfone (VS) reactive group.    -   c) One or more semi-conductor nanoparticles having one or more        distinguishable fluorescence emissions or wavelengths.    -   d) Semi-conductor nanoparticles (c) having at least thiol        functional groups at least on the surface of the particles.    -   e) Spontaneous, covalent coupling of solid support (b) and        semi-conductor nanoparticles (d) to form a stable, covalent        bond.    -   f) Use of the semi-conductor nanoparticles-coupled solid        support (e) for decoding in a single multiplexed assay.

Example 6.3.6

This example relates to, but is not limited to, the covalent coupling offunctionalized, or pre-activated, microspheres to functionalized, orpre-activated nanospheres using a linker or bridge between the twoparticles.

-   -   a) A solid support comprised of a polymeric microsphere,        preferably polystyrene/divinyl-benzene, containing carboxyl        functional groups at least on its surface.    -   b) Solid support (a) where the carboxyl groups have been        modified to contain the novel mono-fluoro squaric acid (MFS)        reactive group.    -   c) Solid support (b) where the novel mono-fluoro squaric acid        (MFS) reactive group has been modified with the bifunctional        linker 4,7,10-trioxa-1,13-tridecanediamine.    -   d) A second solid support comprised of polymeric nanospheres,        preferably polystyrene/divinyl-benzene, containing carboxyl        functional groups at least on its surface.    -   e) Solid support (d) where the carboxyl groups have been        modified to contain the novel mono-fluoro squaric acid (MFS)        reactive group.    -   f) Solid support (e) having one or more fluorescent dyes in        distinguishable ratios.    -   g) Spontaneous, covalent coupling of microsphere solid        support (c) and nanosphere solid support (f) to form a stable,        covalent bond.    -   h) Use of the nanosphere-coupled microsphere solid support (g)        for decoding in a single or multiplexed assay.

Example 6.3.7

This example relates to, but is not limited to, the use offunctionalized, or pre-activated, microspheres for covalentimmobilization of dendrimers.

-   -   a) A solid support comprised of a polymeric microsphere,        preferably polystyrene/divinyl-benzene, containing carboxyl        functional groups at least on its surface.    -   b) The solid support (a) where the solid support contains one or        more fluorescent dyes in distinguishable ratios.    -   c) Solid support (b) where the carboxyl groups have been        modified to contain the novel tetra-fluoro-sulfophenyl ester        (TFS) reactive group.    -   d) A dendrimer containing primary amine functional groups.    -   e) Spontaneous, covalent coupling of solid support (c) and        dendrimer (d) to form a stable, covalent bond.    -   f) Modification of the dendrimer-coupled solid support (e) with        a bifunctional linker containing the novel reactive group        mono-fluoro squaric acid (MFS) on both termini of the linker.    -   g) A biomolecule, specifically an antibody, containing a primary        amine.    -   h) Spontaneous, covalent coupling of solid support (f) and        biomolecule (g) to form a stable, covalent bond.    -   i) Use of the biomolecule-coupled solid support (h) in a single        or multiplexed immunoassay.

Example 6.3.8

This example relates to, but is not limited to, the covalent coupling ofbiomolecules to microspheres via a novel linker.

-   -   a) A solid support comprised of a polymeric microsphere,        preferably polystyrene/divinyl-benzene, containing carboxyl        functional groups at least on its surface.    -   b) The solid support (a) where the solid support contains one or        more fluorescent dyes in distinguishable ratios.    -   c) Solid support (b) where at least surface carboxyl groups have        been modified with a novel bifunctional amine termini linker        containing a least one or more squaric acid functional groups        within the linker chain.    -   d) A biomolecule, specifically an oligonucleotide probe,        containing the novel tetra-fluoro-sulfophenyl ester (TFS)        reactive group at one terminus.    -   e) Spontaneous, covalent coupling of solid support (c) and        biomolecule (d) to form a stable, covalent bond.    -   f) Use of the biomolecule-coupled solid support (e) in a nucleic        acid-based assay, wherein said assay comprises DNA, RNA, PNA,        etc.

Example 6.3.9

This example relates to, but is not limited to, the covalent labeling ofa biomolecule with a functionalized, or pre-activated fluorophore.

-   -   a) A fluorophore functionalized, modified and/or synthesized to        contain the novel reactive group mono-fluoro squaric acid (MFS).    -   b) A biomolecule, specifically avidin, streptavidin,        neutra-avidin and the like containing primary amines.    -   c) Spontaneous, covalent labeling of biomolecule (b) and the        pre-activated fluorophore (a) to form a stable, covalent bond.    -   d) A solid support comprised of a polymeric microsphere,        preferably polystyrene divinyl-benzene, containing biotin        functional groups at least on its surface.    -   e) The solid support (d) where the solid support contains one or        more fluorescent dyes in distinguishable ratios.    -   g) Use of the solid support (e) in a single or multiplexed assay        where the fluorophore-labeled biomolecule (c) is used as a        reporter molecule.

Example 6.3.10

This example relates to, but is not limited to, the use offunctionalized, or pre-activated, biomolecules for the covalentimmobilization onto a solid surface.

-   -   a) A solid support comprised of one or more metals.    -   b) The solid support (a) where the solid support has been        modified with a self-assembled monolayer (SAM) to contain thiol        functional groups.    -   c) A biomolecule, specifically an oligonucleotide, modified        and/or synthesized to contain the novel reactive group vinyl        sulfone (VS) at one terminus.    -   d) Spontaneous, covalent coupling of solid support (b) and        biomolecule (c) to form a stable, covalent bond.    -   e) Use of the biomolecule-coupled solid support (d) in a single        or multiplexed nucleic acid-based assay, wherein said assay        comprises DNA, RNA, PNA, etc.

Example 6.3.11

This example relates to, but is not limited to, the use offunctionalized, or pre-activated, particles for the covalentimmobilization of fluorophores.

-   -   a) Solid support particles comprised of one or more metals.    -   b) The solid support (a) where the solid support has been        modified to contain the novel functional group mono-fluoro        squaric acid (MFS).    -   c) J- or H-aggregate fluorophores containing amines and a        quencher molecule.    -   d) Spontaneous, covalent coupling of solid support (b) and        fluorophore (c) to form a stable, covalent bond.    -   e) Use of the fluorophore-labeled particles (d) as a reporter in        a single or multiplexed assay.

7.0 Examples of Synthetic Procedures for Preparing the Novel ReactiveGroups

Aspects of the invention include materials and procedures for preparingcompositions, conjugates and/or mixtures involving polymer particles,various linkers and functional groups. These linkers and functionalgroups are described as follows: (7.0) synthetic procedures of surfacefunctional groups and spacers, (7.1) evaluation of novel reactivegroups, (7.2) examples of coupling procedures. Such descriptionsprovided herein are not intended to limit the present invention in anyway.

7.0.1. Sulfonyl Chloride

The following describes a method for the preparation of an activatedsurface capable of immobilizing a biomolecule in accordance with thepresent invention. In particular, the following example describes amethod for activating carboxylated polystryene microspheres withsulfonyl chloride groups.

100 μL (approximately 11 million microspheres) of a carboxylatedpolystyrene microsphere solution (5.5 μm) was washed once with 250 μL ofDI water, three times with 250 μL of methanol, and three times with 250μL of benzene using centrifugation at 13,400×g for 1 minute to pelletand 20 seconds of sonication to resuspend the microspheres. Finally theywere suspended in 250 μL of benzene, 50 μL of thionyl chloride was addedand the microspheres were heated at 40° C. for 2 hours. Then themicrospheres were washed two times with 250 μL of benzene and driedunder reduced pressure (<5 torr) for 2 hours. They were suspended in asolution of potassium 7-amino-1,3-disulfonylnaphthalene in 200 μL ofpyridine and kept at room temperature for 4 hours. Then they were washedtwo times with 250 μL of pyridine, four times with 250 μL of DI water,two times with 250 μL of methanol, and two times with 250 μL of benzeneand suspended in a solution of 50 μL thionyl chloride and 25 μL ofdimethylformamide (DMF) in 250 μL of benzene and kept at roomtemperature for 20 minutes and at 40° C. for one hour. Afterwards thereactive microspheres were washed once with 250 μL of benzene and threetimes with 250 μL of acetonitrile and stored in acetonitrile until used.The just described procedure is graphically described in Entry 1c ofTable 1.

7.0.2. Sulfonyl Fluoride

The following describes a method for the preparation of an activatedsurface capable of immobilizing a biomolecule in accordance with thepresent invention. In particular, the following example describes amethod for activating carboxylated polystryene microspheres withsulfonyl fluoride groups.

300 μL (32 million microspheres) of a carboxylated polystyrenemicrosphere solution (5.5 μm) was washed two times with 500 μL of DIwater, two times with 500 μL of methanol, and two times with 500 μL ofbenzene using centrifugation at 13,400×g for 1 minute to pellet themicrospheres and 20 seconds of sonication to resuspend the microspheres.The microspheres were then suspended in a solution of 50 μL thionylchloride in 250 μL of benzene and kept at 40° C. for 2 h. Then they werewashed three times with 500 μL of benzene and two times with 500 μL ofacetonitrile and afterwards suspended in a solution of 12 mg ofpotassium 7-amino-1,3-disulfonylnaphthalene in 500 μL of acetonitrileand placed in a shaker at room temperature. After 14 hours themicrospheres were washed two times with 500 μL of acetonitrile. Themicrospheres were suspended in a solution of acetonitrile containing 15μL of cyanuric fluoride and 20 μL of pyridine and kept at −15° C. for 14h and afterwards washed three times with 500 μL of acetonitrile. Themicrospheres were suspended and stored in 1 ml of acetonitrile. The justdescribed procedure is graphically described in Entry 2b of Table 1.

7.0.3. Mono-fluoro Squaric Acid (MFS)

The following describes a method for the preparation of an activatedsurface capable of immobilizing a biomolecule in accordance with thepresent invention. In particular, the following example describes amethod for activating carboxylated polystryene microspheres withmono-fluoro squaric acid groups using adipic acid dihydrazide as alinker.

300 μL (32 million microspheres) of a carboxylated polystyrenemicrosphere solution (5.5 μm) was washed three times with 500 μL of asolution containing 0.01% Tween 20 and 0.1 M MES buffer, pH 6.0 usingcentrifugation at 13,400×g for 1 minute to pellet the microspheres and20 seconds of sonication to resuspend the microspheres. The microsphereswere then suspended in 500 μL of a solution containing 32 mg/mL of ADH(adipic acid dihydrazide) and 2 g/mL of EDC, 0.01% Tween 20, and 0.1 MMES buffer, pH 6.0 and placed on a rotating mixer for 2 hours protectedfrom light. The microspheres were washed three times with 500 μL ofwater, three times with 500 μL of methanol, and three times with 500 μLof benzene. The microspheres were then suspended in 500 μL of benzeneand 1 μL of dibutoxy cyclobutene dione was added. After shaking on athermal shaker for 14 hours at 25° C., the microspheres were washedthree times with 500 μL of benzene, three times with 500 μL of methanol,and three times with 500 μL of DI water. To the microspheres was added500 μL of a 1 M solution of sodium hydroxide. The microspheres were thenplaced in a thermal shaker for 2 hours at 60° C. Then they were washedwith 500 μL of methanol to recover the microspheres. The microsphereswere then washed with 500 μL of a 2 M solution of hydrochloric acid.Methanol was added to recover the microspheres. The microspheres werethen washed three times with 500 μL of methanol and three times with 500μL of acetonitrile. The microspheres were then suspended in 500 μL ofacetonitrile. A solution of 15 μL of cyanuric fluoride and 20 μL ofpyridine was added and then the microspheres were stored at −15° C. for14 hours. The microspheres were then washed three times with 500 μL ofacetonitrile. The microspheres were suspended and stored in 1 mL ofacetonitrile. The just described procedure is graphically described inEntry 3c of Table 1.

7.0.4. Cyanuric Fluoride

The following describes a method for the preparation of an activatedsurface capable of immobilizing a biomolecule in accordance with thepresent invention. In particular, the following example describes amethod for activating carboxylated polystryene microspheres withcyanuric fluoride using 1,6-diaminohexane as a linker.

300 μL (32 million microspheres) of carboxylated polystyrene microspheresolution (5.5 μm) was washed three times with 500 μL of a solutioncontaining 0.01% Tween 20 and 0.1 M MES buffer, pH 6.0 usingcentrifugation at 13,400×g for 1 minute to pellet the microspheres and20 seconds of sonication to resuspend the microspheres. Afterwards theywere suspended in 500 μL of a solution containing 32 mg/mL of1,6-diaminohexane and 2 g/mL of EDC, 0.01% Tween 20, and 0.1 M MESbuffer, pH 6.0 and placed on a rotating mixer for 2 hours protected fromlight. Subsequently the microspheres were washed three times with 500 μLof water, three times with 500 μL of methanol, and three times with 500μL of acetonitrile. The microspheres were then suspended in a solutioncontaining 500 μL of acetonitrile, 20 μL of trimethyl amine and 15 μl,of cyanuric fluoride and was set for 14 hours at −15° C. Finally theywere washed three times with acetonitrile. The microspheres weresuspended and stored in 1 mL of acetonitrile. The just describedprocedure is graphically described in Entry 4 of Table 1.

7.0.5. Vinyl Sulfone (VS)

The following describes a method for the preparation of an activatedsurface capable of immobilizing a biomolecule in accordance with thepresent invention. In particular, the following example describes amethod for activating carboxylated polystryene microspheres with vinylsulfone (VS) using-2-aminoethanethiol as a linker.

300 μL (32 million microspheres) of a carboxylated polystyrenemicrosphere solution (5.5 μm) was washed three times with 500 μL of 0.1M MES buffer, pH 6.0 incl. 0.01% Tween 20 using centrifugation at13,400×g for 1 minute to pellet the microspheres and 20 seconds ofsonication to resuspend the microspheres. Subsequently the microsphereswere suspended in 500 μL of a 16 mg/mL solution of cysteamine and 30mg/mL solution of EDC in 0.01% Tween 20, 0.1 M MES buffer, pH 6.0 andplaced on a rotating mixer protected from light for 2 hours. Themicrospheres were washed three times with 500 μL of water and threetimes with 500 μL of 0.1M sodium chloride/0.1 M sodium acetate buffer,pH 4.5. The disulfide bonds of the bound cysteamine groups were reducedby suspending the microspheres in 500 μL of a 11 mg/mL solution ofdithiothreitol (DTT) in 0.1 M sodium acetate/0.1 M sodium chloridebuffer, pH 4.5. The microspheres were placed on a rotating mixer for 30minutes and afterwards washed three times with 500 μL of methanol. Thenthey were suspended in 500 μL of dichloromethane and 5 μL of vinylsulfone (VS) was added. After mixing on a rotating mixer for 14 hours,500 μL of methanol was added and the microspheres were recovered andwashed three times with 500 mL of methanol. The microspheres weresuspended and stored in 1 mL of methanol. The just described procedureis graphically described in Entry 5b of Table 1.

7.0.6. Protected Vinyl Sulfone

The following describes a method for the preparation of an activatedsurface capable of immobilizing a biomolecule in accordance with thepresent invention. In particular, the following example describes amethod for converting the activated polystyrene microspheres of theprevious example into a more hydrolysis resistant form.

Microspheres prepared according to Example 5.0.5 were suspended in 800μL of a solution containing 3 mg of sodium thiosulfite, 0.01% Tween 20,and sodium phosphate buffer, pH 4.0 for 14 hours. The microspheres werewashed three times with 500 μL of DI water. The microspheres weresuspended and stored in 1 mL of DI water. The microspheres are notreactive with nucleophiles unless they are first treated with a bufferof pH 9-10. The just described procedure is graphically described: inEntry 5c of Table 1.

7.0.7. Tetra-fluoro sulfo-phenyl Ester (TFS)

The following describes a method for the preparation of an activatedsurface capable of immobilizing a biomolecule in accordance with thepresent invention. In particular, the following example describes amethod for directly activating carboxylated polystryene microsphereswith tetra-fluoro sulfophenyl esters.

300 μL (32 million microspheres) of a carboxylated polystyrenemicrosphere solution (5.5 μm) was washed three times with 500 μL of asolution containing 0.01% Tween 20 and 0.1 M MES buffer, pH 6.0 usingcentrifugation at 13,400×g for 1 minute to pellet and 20 seconds ofsonication to resuspend the microspheres. Then they were suspended in500 μL of a solution containing 24 mg/mL of 2,3,5,6tetrafluorophenol-4-sulfate (synthesized from 2,3,5,6 tetrafluorophenolaccording to the procedure of Gee, K. R. et al. Tetrahedron Lett., 1999,40, 1472-1474), 220 mg/mL of EDC, 0.01% Tween 20, and 0.1 M MES buffer,pH 6.0 and then placed on a rotating mixer protected from light for 2hours. The microspheres were washed three times with 500 μL of DI water.The microspheres were suspended and stored in 1 mL of DI water. The justdescribed procedure is graphically described in Entry 6 of Table 1.

7.1. Examples of Novel Reactive Group Evaluation

In order to quantify the reactivity of the different novel reactivefunctional groups on polystyrene microspheres, a simple assay wasdeveloped using a biotin-amine derivative. First, biotin-LC-PEO-amine(obtained from Pierce, Rockford, Ill.) was coupled to carboxylatedmicrospheres using typical EDC-mediated methods, followed by reactionwith streptavidin-PE. The optimum concentrations of both biotin-amineand streptavidin-PE (obtained from Molecular Probes, Eugene, Oreg.) weretitrated. This coupling assay provided a “standard” by which to measureand compare the reactivity of microspheres modified with the novelreactive functional groups. The modified microspheres are evaluated byreacting the biotin-amine directly, followed by reaction withstreptavidin-PE. Functional group stability was evaluated by storing themicrospheres either in buffer (pH 6; 4° C.) or dry, and performing thebiotin-LC-PEO-amine assay at set intervals (e.g., days, weeks, months,etc.).

According to our test results our new novel reactive groups exhibit verydesirable properties. For example, novel reactive groups show goodreactivity with nucleophilic compounds, have substantially improvedstability in aqueous media, form stable conjugates, require noadditional activating reagents (e.g., EDC and/or NHS esters), and mayprovide more specific conjugation (i.e., reduce non-specificinteraction/binding with solid substrates) thus protecting the integrityof biomolecules.

7.1.1 Coupling Reactivity and Reproducibility

An accelerated stability study comparing the EDC-mediated couplingmethod to mono-fluoro squaric acid (MFS)-modified microspheres wascarried out over an equivalent of 350 days. Using the biotin-amine modelassay, results showed comparable reactivity between the two methods.Results also show the mono-fluoro squaric acid (MFS)-modifiedmicrospheres provide more reproducible coupling day-to-day. As depictedin FIG. 1, the EDC coupling method showed 20% changes in couplingthroughout the entire experiment. During the equivalent 350 days, themono-fluoro squaric acid (MFS)-modified microspheres lost some activitygradually, retaining 80% activity at the end of the study (i.e., thegreatest change in activity was shown at the end of 350 equivalentdays). Improvements in storage procedures are expected to eliminate anyloss of activity for modified microspheres.

7.1.2 Stability

Results show that microspheres modified with novel reactive groups havesubstantially improved stability in aqueous media. FIG. 2 depicts anexample of the stability of vinyl-sulfone (VS)-functionalizedmicrospheres in buffer for at least 30 days. This is a substantialimprovement compared to EDC and NHS reagents, however, since there is atrade-off between reactivity and stability, we have also evaluatedvarious drying and storage methods for long-term storage (including forexample, 6 months, ≧approximately 6 months, greater than six months, sixmonths to nine months, six months to one year, six months to two years,etc.) of the modified microspheres. FIGS. 3-6 depict examples of drystorage condition stability studies. Storage vessels that providesuperior moisture barrier properties to those used in this study, willprevent loss of activity over time.

7.1.3 Bioassays

The performance of modified microspheres in real-assays compared to theCOOH microsphere-EDC method was evaluated. FIG. 7 shows a couplingtitration of an amino-modified DNA probe on COOH-functionalizedmicrospheres (EDC-mediated reaction) vs. pre-activated microspheremethod. Both coupling titrations were performed at 25° C. The DNAcompliment target concentration for the assay was 20 fmoles at ahybridization temperature of 55° C. Results show the COOH-EDC methodyields a non-linear response to the amount of probe coupled to themicrosphere. The pre-activated microsphere probe titration is morelinear, suggesting a more specific coupling of the probe. Both resultsare reproducible. Note: 25° C. is not an optimal coupling temperaturefor the pre-activated microspheres. The signal is expected to improvewith optimization of coupling temperature, as well as other parameters.

7.2 Examples of Coupling Procedures 7.2.1. Biotin-LC-PEO Amine

Surface-modified microspheres were washed three times with phosphatebuffer (pH 6, 100 mM) and counted. 2.5×10⁷ microspheres were aliquotedand washed once with phosphate buffer (pH 8, 100 mM). A solution ofPEO-LC-biotin-amine (17.4 mg/mL) was prepared in phosphate buffer (pH 8,100 mM). 100 μL of this solution was added to the microspheres, in 900μL phosphate buffer (pH 8, 100 mM). The suspension was incubated at 37°C. for 1 hour. After the reaction was complete, the microspheres werewashed three times with PBS-TBN (phosphate buffered saline, pH 7.4 with0.02% Tween 20 and 1 g/L bovine serum albumin), and recounted. Asuspension of 100,000 microspheres/mL PBS-TBN was reacted with 1 μgStreptavidin-PE for 1 hour at room temperature. Subsequently themicrospheres were washed three times and resuspended in 1 mL PBS-TBN.The fluorescence intensity of the microspheres was analyzed on a Luminex100™ instrument.

7.2.2. Biotinylated IgG

A suspension of 25×10⁶ surface-modified microspheres was washed with 1mL carbonate buffer (pH 9, 100 mM). A 1 mL solution of IgG (50 μg/mL in0.1 M pH 9 carbonate buffer) was added to the microspheres, vortexed,sonicated and incubated at 37° C. for 1 hour. After 1 hour, the samplewas washed with 1 mL PBS-TBN (phosphate buffered saline, pH 7.4 with0.02% Tween 20 and 1 g/L bovine serum albumin). A suspension of 100,000microspheres/mL PBS-TBN was reacted with 1 μg Streptavidin-PE for 1 hourat room temperature. Subsequently the microspheres were washed threetimes and resuspended in 1 mL PBS-TBN. The fluorescence intensity of themicrospheres was analyzed on a Luminex 100™ instrument.

7.2.3. Biotinylated Oligonucleotides

5×10⁶ surface-modified microspheres were dispensed into a 1.5 mlcentrifuge tube and washed with 1 mL of carbonate buffer (pH 9, 100 mM).50 μL carbonate buffer (pH 9, 100 mM) was added to the microspheres. 1μL of a 1 mM solution of amino-modified oligonucleotide was added andthe suspension was incubated at 37° C. for 1 hour. After 1 hour thesample was washed with PBS-TBN. A suspension of 100,000 microspheres/mLPBS-TBN was reacted with 1 μg Streptavidin-PE for 1 hour at roomtemperature. Subsequently the microspheres were washed three times andresuspended in 1 mL PBS-TBN. The fluorescence intensity of themicrospheres was analyzed on a Luminex 100™ instrument.

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. Such equivalents areintended to be encompassed by the following claims.

TABLE 1 Summary of Functional Groups and Synthetic Routes toFunctionalized Microspheres 1a

1b

1c

1d

2a

2b

2c

2d

2e

3a

3b

3c

3d

3e

4

5a

5b

5c

6

TABLE 2 Summary Representative Linker Groups R_(n) 1.

2.

3.

4.

5.

6.

7.

8.

9.

10.

11.

12.

13.

14.

15.

16.

17.

1.-3. (canceled)
 4. A bridge group composition comprising two or moredifferent structures, in any combination, of Structures 1-6:

wherein: n is 0, 1, 2, or 3; X and Y are oxygen and/or sulfur in anycombination; X₂ and X₃ are chlorine or fluorine; Y₂ is nitrogen orcarbon; arom is a substituted or unsubstituted phenyl, naphthyl or otherpolycyclic aromatic ring structure; Z is chloride, fluoride,2,3,5,6-tetrafluoro-4-sulfo-phenoxide, N-hydroxysuccinimide or otherelectrophilic group; and R₁-R₆ comprise hydrocarbon linker groupscontaining from 2-1000 atoms, optionally containing one or more halogenor heteroatoms selected from the group consisting of O, N, Si, P and S;wherein the two or more different structures are joined together throughtheir respective linker groups R₁-R₆, and wherein said joining is one ormore of end-to-end, branched, or dendritic, in any combination. 5.-7.(canceled)
 8. The bridge group composition of claim 4, wherein thelinker groups R₁-R₆ are straight or branched chains, rings, orcombinations thereof
 9. The bridge group composition of claim 4, whereinR₁-R₆ contain 2-100 atoms
 10. The bridge group composition of claim 4,wherein R₁-R₆ contain 2-10 atoms.
 11. The bridge group composition ofclaim 4, wherein at least one of the linker groups is alkyl glycolbased.
 12. The bridge group composition of claim 4, wherein at least oneof the linker groups is a fluorinated alkyl glycol comprising between 1and 6 carbon atoms.
 13. The bridge group composition of claim 4, whereinat least one of the linker groups is selected from a group consisting ofdiamines and di-hydrazides.
 14. The bridge group composition of claim 4,wherein at least one of the linker groups comprises a polyethylenimine.15. The bridge group composition of claim 4, wherein at least one of thelinker groups is selected from a group consisting of polyamides andpolysulfonamides.
 16. The bridge group composition of claim 4, whereinat least one of the linker groups comprises a dendrimer.
 17. The bridgegroup composition of claim 4, wherein at least one of the linker groupscomprises a diethylene triamine pentaacetic acid.
 18. The bridge groupcomposition of claim 4, wherein at least one of the linker groups isselected from a group consisting of polyacrylic acid and polylysinechains.
 19. The bridge group composition of claim 4, wherein the linkergroup R₁ comprises one or more halogen atoms.
 20. The bridge groupcomposition of claim 4, wherein the linker group R₁ comprises one ormore heteroatoms selected from the group consisting of O, N, Si, P andS.
 21. The bridge group composition of claim 4, further comprising atleast one entity connected to the joined structures, wherein the atleast one entity is: a 2-D film or substrate; a micro- or nano-particleof any size or shape composed of organic polymer, MIPS, glass, metal,clay, resin, diatomaceous earth, zeolite, inorganic crystal,semiconductor particle, semiconductor nanocrystal, magnetic particle,fullerene, nanotube, or any combination thereof; an enzyme, antibody,protein, DNA, RNA, nucleotide, PNA, carbohydrate, fatty acid, lectin,peptide, receptor, dendrimer, cell, bacteria, virus, whole prokaryoticor eukaryotic organism, synthetic or natural membrane, biotin, hapten,organic monomer or polymer, or any combination thereof; a chromophore,fluorophore, bio- or chemi-luminescent compound, J or H aggregate, orany combination thereof; one or more of Structures 1-6, in anycombination, connected through their respective linker groups R₁-R₆; orany combination thereof.
 22. The bridge group composition of claim 21,wherein the at least one entity is connected to the joined structures bya branched linker.
 23. The bridge group composition of claim 21, whereinthe micro- or nano-particle further comprises one or more fluorescentdyes in differing, distinguishable molar amounts.
 24. The bridge groupcomposition of claim 21, wherein the at least one entity comprises apolymeric microsphere or a polymeric nanosphere, wherein the polymericsphere further comprises at least one of an amino functional group, athiol functional group, and a hydroxyl functional group at least on itssurface.
 25. The bridge group composition of claim 4, further comprisinga biomolecule connected to at least one of the two or more of Structures1-6, wherein the biomolecule is selected from a group consisting ofprokaryotic cells, eukaryotic cells, transgenic cells, organisms,bacteria, viruses, plasmids, expression vectors, enzymes, proteins,fusion proteins, antibodies, chimeric antibodies, DNA, RNA, PNA, fattyacids, lectins, peptides, and receptors, or any combination thereof. 26.The bridge group composition of claim 4, wherein at least two structuresof the two or more Structures 1-6 are conjugated by their respectivelinker groups R₁-R₆ to one or more nucleophilic groups.